This paper presents a new numerical method for optical tomography: the combined boundary element/finite element method (BEM-FEM), designed to tackle reconstructions in layered turbid media. The BEM-FEM focuses on the region of interest by creating a volume mesh and reconstructing in this region only. All other regions are treated as piecewise constant in a surface-integral approach. We validate the model in concentric spheres, with different positions of the volume-integral treated area and found it compared well with an analytical result. We then performed functional imaging of the neonate's motor cortex in vivo, in a reconstruction restricted to the brain, both with FEM and BEM-FEM. These results show the effectiveness of the BEM-FEM in situations where the organ of interest is surrounded by superficial layers.